In July 2002, he became the Acting Co-Director of the California NanoSystems Institute (CNSI). In May 2003, he became the Fred Kavli Chair of NanoSystems Sciences and served from then through August 2007 as the Director of the CNSI. He was appointed a Knight Bachelor in the New Year's Honours December 2006, by Queen Elizabeth II.[6] In 2007, he received the Albert Einstein World Award of Science in recognition for his outstanding and pioneering work in molecular recognition and self-assembly, and the introduction of quick and efficient template-directed synthetic routes to mechanically interlocked molecular compounds, which have changed the way chemists think about molecular switches and machines.[7]

Stoddart's papers and other material are instantly recognizable due to a distinctive "cartoon"-style of representation he has developed since the late 1980s. A solid circle is often placed in the middle of the aromatic rings of the molecular structures he has reported, and different colors to highlight different parts of the molecules. Indeed, he was one of the first researchers to make extensive use of color in chemistry publications. The different colors usually correspond to the different parts of a cartoon representation of the molecule, but are also used to represent specific molecular properties (blue, for example, is used to represent electron-poor recognition units while red is used to represent the corresponding electron-rich recognition units). Stoddart maintains this standardized color scheme across all of his publications and presentations, and his style has been adopted by other researchers reporting mechanically interlocked molecules based on his syntheses.